MsaMultipleAnlignmentClasses {msa} | R Documentation

## Classes `MsaAAMultipleAlignment`, `MsaDNAMultipleAlignment`, and `MsaRNAMultipleAlignment`

### Description

S4 classes for storing multiple alignments of amino acid, DNA, and RNA sequences along with algorithm metadata

### Objects

Objects of these classes are returned by the multiple sequence alignment algorithms `msaClustalW`, `msaClustalOmega`, `msaMuscle`, and the wrapper function `msa`, all of which are provided by the msa package.

### Details

The class `MsaAAMultipleAlignment` extends the `AAMultipleAlignment` class, the class `MsaDNAMultipleAlignment` extends the `DNAMultipleAlignment` class, and the class `MsaRNAMultipleAlignment` extends the `RNAMultipleAlignment` class. All three classes extend their parent classes by the slots contained in the `MsaMetaData`, i.e. all three classes are class unions of the aforementioned parent classes and the class `MsaMetaData`.

### Methods

`print(x, show=c("alignment", "version", "call"), showNames=TRUE, showConsensus=TRUE, halfNrow=9, nameWidth=20, ...)`:

  prints information about the object `x`; the `show` argument allows for determining what should be printed. The `show` must be a character vector and may contain any combination of the following strings: if `show` contains `"alignment"`, the multiple sequence alignment is printed in a way similar to the corresponding method from the Biostrings package (except for the consensus sequence, see below). If `show` contains `"complete"`, the entire width of the alignment is printed by splitting it over multiple blocks of lines if necessary. This overrules `"alignment"` if both are contained in the `show` argument. If `show` contains `"version"`, the `version` slot is shown. If `show` contains `"call"`, the `call` slot is shown. If `show` contains `"standardParams"`, the settings of the parameters that are common to all three multiple sequence alignment algorithms are shown. If `show` contains `"algParams"`, the algorithm-specific parameters are shown. The order in which the strings are placed in the `show` argument does not have an effect on the order in which data are printed. The default is `show=c("alignment", "version", "call")`, i.e. by default, the multiple sequence alignment is shown along with version and call information. If `show` contains `"all"`, the complete alignment is shown along with version information, call, and the complete set of parameters. As said above, by default, printing alignments is similar to the standard `print` method provided by the Biostrings package, whereas including `"complete"` in the argument `show` prints the entire width of the alignment. Unlike the method from the Biostrings package, the appearance can be customized: by default, the consensus sequence is appended below the alignment. To switch this off, use `showConsensus=FALSE`. Whether or not sequence names should be printed can be controlled via the `showNames` argument. The width reserved for the sequence names can be adjusted using the `nameWidth` argument; the default is 20 like in the Biostrings method. If the number of sequences in the alignment is large, output can become quite lengthy. That is why only the first `halfNrow` and the last `halfNrow` sequences are shown. To show all sequences, set `halfNrow` to `NA` or -1. Note that `print` can also handle masked objects, where the masked sequences/positions are shown as hash marks. However, the consensus sequences are computed from the complete, unmasked alignment and displayed as such. Additional arguments are passed on to `msaConsensusSequence` for customizing how the consensus sequence is computed.

`show(object)`:

  displays the alignment along with metadata; synonymous to calling `print` with default arguments.

`version(object)`:

  displays the algorithm with which the multiple alignment has been computed along with its version number (see also `MsaMetaData`).

`params(x)`:

  accessor to the `params` slot (see also `MsaMetaData`)

### Author(s)

Enrico Bonatesta, Christoph Horejs-Kainrath, and Ulrich Bodenhofer <msa@bioinf.jku.at>

### References

http://www.bioinf.jku.at/software/msa

U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.

### See Also

`msa`, `msaClustalW`, `msaClustalOmega`, `msaMuscle`, `MsaMetaData`

### Examples

    ## read sequences
    filepath <- system.file("examples", "exampleAA.fasta", package="msa")
    mySeqs <- readAAStringSet(filepath)

    ## simple call with default values
    myAlignment <- msaClustalOmega(mySeqs)

    ## show the algorithm version with which the results were created
    version(myAlignment)

    ## show the results
    show(myAlignment)

    ## print the results
    print(myAlignment, show="alignment")
    print(myAlignment, show="alignment", showConsensus=FALSE)
    print(myAlignment, show=c("alignment", "version"))
    print(myAlignment, show="standardParams")
    print(myAlignment, show="algParams")
    print(myAlignment, show=c("call", "version"))

    ## print results with custom consensus sequence
    print(myAlignment, show="complete", type="upperlower", thresh=c(50, 20))

    ## show the params
    params(myAlignment)

[Package msa version 1.19.0 Index]